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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100932
|fonse_cell_line=FF:0100932
|fonse_cell_line_closure=FF:0100932
|fonse_cell_line_closure=FF:0100932

Revision as of 16:54, 29 March 2012


Name:neuroblastoma cell line:NH-12
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexunknown
ageNA
cell typeneuroblast
cell lineNH-12
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.045
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0.0858
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.364
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.536
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11811

Jaspar motifP-value
MA0002.25.80545e-4
MA0003.10.143
MA0004.10.343
MA0006.10.0787
MA0007.10.0992
MA0009.10.141
MA0014.10.473
MA0017.10.00118
MA0018.20.0026
MA0019.10.429
MA0024.12.30812e-6
MA0025.10.596
MA0027.10.801
MA0028.10.159
MA0029.10.77
MA0030.10.929
MA0031.10.282
MA0035.20.543
MA0038.11.04065e-4
MA0039.20.0502
MA0040.10.247
MA0041.10.225
MA0042.10.5
MA0043.10.062
MA0046.10.344
MA0047.20.0752
MA0048.10.581
MA0050.14.50675e-9
MA0051.11.17488e-4
MA0052.10.00786
MA0055.10.816
MA0057.10.114
MA0058.10.358
MA0059.10.309
MA0060.15.23619e-14
MA0061.10.0121
MA0062.20.165
MA0065.20.0032
MA0066.10.059
MA0067.10.945
MA0068.10.529
MA0069.10.779
MA0070.10.499
MA0071.10.194
MA0072.10.342
MA0073.10.259
MA0074.10.0991
MA0076.10.0173
MA0077.10.104
MA0078.10.572
MA0079.20.205
MA0080.21.49944e-11
MA0081.10.197
MA0083.10.0646
MA0084.10.403
MA0087.10.184
MA0088.10.444
MA0090.10.0115
MA0091.10.369
MA0092.10.224
MA0093.10.252
MA0099.25.44045e-19
MA0100.10.516
MA0101.10.0304
MA0102.20.0137
MA0103.10.0718
MA0104.20.0386
MA0105.10.0289
MA0106.10.301
MA0107.10.00763
MA0108.20.458
MA0111.10.918
MA0112.21.31793e-4
MA0113.10.102
MA0114.10.0283
MA0115.10.673
MA0116.10.0167
MA0117.10.978
MA0119.10.136
MA0122.10.373
MA0124.10.691
MA0125.10.143
MA0131.10.383
MA0135.10.527
MA0136.11.9431e-8
MA0137.20.194
MA0138.20.686
MA0139.10.44
MA0140.10.425
MA0141.10.00674
MA0142.10.736
MA0143.10.945
MA0144.10.0113
MA0145.10.101
MA0146.10.0593
MA0147.10.0544
MA0148.10.031
MA0149.10.0423
MA0150.17.9425e-5
MA0152.10.671
MA0153.10.154
MA0154.10.0339
MA0155.10.459
MA0156.10.0022
MA0157.10.0729
MA0159.10.00353
MA0160.10.0181
MA0162.10.253
MA0163.10.0194
MA0164.10.945
MA0258.10.00816
MA0259.10.0551



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11811

Novel motifP-value
10.22
100.309
1000.913
1010.549
1020.739
1030.175
1040.517
1050.406
1060.00363
1070.0196
1080.678
1090.0211
110.0948
1100.268
1110.655
1120.105
1130.691
1140.0894
1150.936
1160.344
1170.214
1180.68
1190.328
120.588
1200.233
1210.972
1220.941
1230.251
1240.472
1250.819
1260.0746
1270.166
1280.047
1290.167
130.0804
1300.612
1310.338
1320.805
1330.558
1340.804
1350.45
1360.565
1370.369
1380.986
1390.426
140.614
1400.383
1410.615
1420.717
1430.0597
1440.812
1450.152
1460.605
1470.547
1480.0153
1490.064
150.206
1500.266
1510.337
1520.0181
1530.723
1540.942
1550.491
1560.637
1570.398
1580.109
1590.00873
160.106
1600.374
1610.919
1620.747
1630.289
1640.166
1650.178
1660.755
1670.416
1680.0574
1690.0187
170.114
180.429
190.14
20.224
200.898
210.283
220.142
230.014
240.135
250.76
260.0536
270.242
280.637
290.213
30.173
300.302
310.576
320.00294
330.348
340.415
350.929
360.799
370.0782
380.285
390.147
40.545
400.204
410.174
420.491
430.134
440.13
450.246
460.185
470.458
480.211
490.304
50.156
500.483
510.427
520.105
530.884
540.188
550.107
560.355
570.906
580.287
590.0204
60.971
600.0219
610.282
620.149
630.18
640.669
650.119
660.47
670.872
680.134
690.345
70.253
700.0081
710.0608
720.225
730.0213
740.241
750.333
760.973
770.0425
780.239
790.0709
80.156
800.0705
810.434
820.225
830.0662
840.605
850.0194
860.409
870.0227
880.671
890.0534
90.165
900.364
910.175
920.0511
930.718
940.223
950.0528
960.257
970.549
980.635
990.377



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11811


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0002321 (embryonic cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
169 (neuroendocrine tumor)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000010 (peripheral nervous system)
0000013 (sympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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